NAME

     obgrep — an advanced molecular search program using SMARTS

SYNOPSIS

     obgrep [OPTIONS] 'SMARTS-pattern' filename

DESCRIPTION

     The obgrep tool can be used to search for molecules inside multi-molecule database files
     (e.g., SMILES, SDF, etc.) or across multiple files.

OPTIONS

     If only a filename is given, obgrep will attempt to guess the file type from the filename
     extension.

     -c    Print the number of matches

     -f    Full match, print matching-molecules only when the number of heavy atoms is also equal
           to the number of atoms in the SMARTS pattern

     -i format
           Specifies input and output format, see obabel(1) for available formats

     -n    Only print the name of the molecules

     -t #  Print a molecule only if the pattern occurs # times inside the molecule

     -v    Invert the matching, print non-matching molecules

EXAMPLES

     Note that in all examples, the SMARTS pattern is enclosed in single quotes '...' to ensure
     it is not changed by the shell.

     Print all the molecules with a methylamine group:
           obgrep 'CN' database.smi

     Print all the molecules without a methylamine group:
           obgrep -v 'CN' database.smi

     Print the number of molecules without a methylamine group:
           obgrep -v -c 'CN' database.smi

     Print methylamine (if it exists in the file):
           obgrep -f 'CN' database.smi

     Print methylamine and/or methanol (if they exist):
           obgrep -f 'C[N,O]' database.smi
     Print all molecules with aromatic carbon in all SMILES files in the directory (i.e., *.smi)
           obgrep 'c' *.smi

SEE ALSO

     obabel(1), obfit(1), obrotate(1).

     The web pages for Open Babel can be found at: <http://openbabel.org/>

     A guide for constructing SMARTS patterns can be found at:
     <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>

AUTHORS

     The obgrep program was contributed by Fabien Fontaine

     Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison,
     Chris Morley, Michael Banck, and innumerable others who have contributed fixes and
     additions.  For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

COPYRIGHT

     Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
     Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other contributors.

     This program is free software; you can redistribute it and/or modify it under the terms of
     the GNU General Public License as published by the Free Software Foundation version 2 of the
     License.

     This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
     without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
     See the GNU General Public License for more details.